Help me with my story? Setting & time period?

I'm planning on writing a novel about a boy and his lover who discover that her parents are part of an illegal time travel project and have tampered with peoples lives. This is a top secret organization and consists of a couple hundred scientists (I think...still debating whether it's possible to have that large a number of people in an organization and still keep it secret). Anyway, it's also secret from the government (hence illegal). Where should this story take place? What time period? I'm not sure if this should be set in the US because I don't think an organization like this could snoop around under our government's noses. What do you think? I'm open to any suggestions!